Code for this DE analysis can be found at maple.sgc.loc/home/bp2582/projects/eye-reg_rnaseq/github/SnailEyeReg_RNASeq/code/DEAnalysis_cond-cutoff.Rmd.

After performing the analysis using as cutoffs adj p-val(FDR) >= 1e-5 and logFC >= |2|, I realized the amount of obtained genes was very little. I don’t think it’s a good idea to loose the pval cutoff since we want to be very confident of the genes we obtain. For that reason, I changed the logFC cutoff to >= 0 in the comparisons that gave us less than 100 genes upregulated or downregulated.

MA plots

With intact eye as a baseline









Paiwise comparisons









Volcano plots

With intact eye as a baseline

3dpa-intact

6dpa-intact

6dpa-intact

9dpa-intact

12dpa-intact

15dpa-intact

21dpa-intact

28dpa-intact

Paiwise comparisons

3dpa-1dpa

6dpa-3dpa

9dpa-6dpa

12dpa-9dpa

15dpa-12dpa

21dpa-15dpa

28dpa-21dpa

intact-28dpa

Gene lists

Can be found at maple.sgc.loc/home/bp2582/projects/eye-reg_rnaseq/github/SnailEyeReg_RNASeq/data/tables/DEAnalysis/DEGenes/cond-cutoff/de/

Number of DE genes

Code in maple.sgc.loc/home/bp2582/projects/eye-reg_rnaseq/github/SnailEyeReg_RNASeq/code/PlotDE-ct_logFC2-1e-5.Rmd.



This list of genes will be used for GO term analysis.